I know this reply is too late to help you, but for anyone wanting to do a negative scale, I think the following example should work. However, the coordinate system will continue to be positive, so you'll just have to convert your positions to positive values (ie. abs(minimum value on scale - feature pos) + 1). For example, the -63 relative to the TSS will be need to be converted to:
abs(-300 - - 63) + 1 = 238
The following code creates the feature and the panel:
my $full_length = Bio::SeqFeature::Generic->new(
                                                -start => 1,
                                                -end   => 300
                                               );


my $panel = Bio::Graphics::Panel->new(
                                      -length    => $length,
                                      -width     => 1000,
                                      -pad_left  => 10,
                                      -pad_right => 10,
                                     );

[download]
This next statement adds the arrow track to the panel, the relative coords needs to be set to true and the relative coords offset is set to the minimum value you want represented on arrow track (in this example it is -300). 
$panel->add_track($full_length,
                  -glyph   => 'arrow',
                  -tick    => 2,
                  -fgcolor => 'black',
                  -double  => 1,
                  -relative_coords => 1,
                  -relative_coords_offset => -300
                 );

[download]
Hope that helps someone,
Lauren

In reply to Re: Bio::Graphics - Howto Enable Neg Start-End, Connector, Create Legend by lbragg
in thread Bio::Graphics - Howto Enable Neg Start-End, Connector, Create Legend by monkfan

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